Preheat your oven to 325°F (165°C). In a large Dutch oven or heavy-bottomed pot over medium heat, cook the diced bacon until crispy. Remove the bacon with a slotted spoon and set it aside, leaving the rendered fat in the pot.

Pat the beef cubes completely dry with paper towels and season generously with salt and pepper. Increase the heat to medium-high. Working in batches, sear the beef in the bacon fat until deeply browned on all sides. Do not overcrowd the pan. Transfer the seared beef to the plate with the bacon.

Reduce the heat to medium. Add the chopped onion and carrots to the pot and cook, stirring occasionally, until softened, about 8-10 minutes. Add the minced garlic and cook for another minute until fragrant.

Return the seared beef and bacon to the pot. Sprinkle the flour over the meat and vegetables and stir until everything is lightly coated. Cook for 1 minute.

Slowly pour in the red wine and beef broth, stirring and scraping the bottom of the pot to release any browned bits (the fond). Stir in the tomato paste, thyme, and bay leaf. Bring the mixture to a gentle simmer.

Cover the pot and transfer it to the preheated oven. Braise for 2.5 to 3 hours, or until the beef is fork-tender.

About 20 minutes before the stew is done, melt the butter in a large skillet over medium-high heat. Add the mushrooms and pearl onions and cook, stirring occasionally, until they are golden brown and tender. Season with salt and pepper.

Carefully remove the stew from the oven. Discard the bay leaf. Gently stir in the cooked mushrooms and pearl onions. Season the Boeuf Bourguignon with more salt and pepper to taste. Garnish with fresh parsley before serving.